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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC

# Line 1 | Line 1
1 + #include <math.h>
2 +
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 27 | Line 29 | template<typename T> NVT<T>::NVT ( SimInfo *theInfo, F
29    have_chi_tolerance = 0;
30    integralOfChidt = 0.0;
31  
30 –  // retrieve chi and integralOfChidt from simInfo
31 –  data = info->getProperty(CHIVALUE_ID);
32 –  if(data){
33 –    chiValue = dynamic_cast<DoubleData*>(data);
34 –  }
32  
33 <  data = info->getProperty(INTEGRALOFCHIDT_ID);
37 <  if(data){
38 <    integralOfChidtValue = dynamic_cast<DoubleData*>(data);
39 <  }
33 >  if( theInfo->useInitXSstate ){
34  
35 <  // chi and integralOfChidt should appear by pair
36 <  if(chiValue && integralOfChidtValue){
37 <    chi = chiValue->getData();
38 <    integralOfChidt = integralOfChidtValue->getData();
35 >    // retrieve chi and integralOfChidt from simInfo
36 >    data = info->getProperty(CHIVALUE_ID);
37 >    if(data){
38 >      chiValue = dynamic_cast<DoubleData*>(data);
39 >    }
40 >    
41 >    data = info->getProperty(INTEGRALOFCHIDT_ID);
42 >    if(data){
43 >      integralOfChidtValue = dynamic_cast<DoubleData*>(data);
44 >    }
45 >    
46 >    // chi and integralOfChidt should appear by pair
47 >    if(chiValue && integralOfChidtValue){
48 >      chi = chiValue->getData();
49 >      integralOfChidt = integralOfChidtValue->getData();
50 >    }
51    }
52  
53 <  oldVel = new double[3*nAtoms];
54 <  oldJi = new double[3*nAtoms];
53 >  oldVel = new double[3*integrableObjects.size()];
54 >  oldJi = new double[3*integrableObjects.size()];
55   }
56  
57   template<typename T> NVT<T>::~NVT() {
# Line 67 | Line 73 | template<typename T> void NVT<T>::moveA() {
73  
74    instTemp = tStats->getTemperature();
75  
76 <  for( i=0; i<nAtoms; i++ ){
76 >  for( i=0; i < integrableObjects.size(); i++ ){
77  
78 <    atoms[i]->getVel( vel );
79 <    atoms[i]->getPos( pos );
80 <    atoms[i]->getFrc( frc );
78 >    integrableObjects[i]->getVel( vel );
79 >    integrableObjects[i]->getPos( pos );
80 >    integrableObjects[i]->getFrc( frc );
81  
82 <    mass = atoms[i]->getMass();
82 >    mass = integrableObjects[i]->getMass();
83  
84      for (j=0; j < 3; j++) {
85        // velocity half step  (use chi from previous step here):
# Line 82 | Line 88 | template<typename T> void NVT<T>::moveA() {
88        pos[j] += dt * vel[j];
89      }
90  
91 <    atoms[i]->setVel( vel );
92 <    atoms[i]->setPos( pos );
91 >    integrableObjects[i]->setVel( vel );
92 >    integrableObjects[i]->setPos( pos );
93  
94 <    if( atoms[i]->isDirectional() ){
94 >    if( integrableObjects[i]->isDirectional() ){
95  
90 –      dAtom = (DirectionalAtom *)atoms[i];
91 –
96        // get and convert the torque to body frame
97  
98 <      dAtom->getTrq( Tb );
99 <      dAtom->lab2Body( Tb );
98 >      integrableObjects[i]->getTrq( Tb );
99 >      integrableObjects[i]->lab2Body( Tb );
100  
101        // get the angular momentum, and propagate a half step
102  
103 <      dAtom->getJ( ji );
103 >      integrableObjects[i]->getJ( ji );
104  
105        for (j=0; j < 3; j++)
106          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
107  
108 <      this->rotationPropagation( dAtom, ji );
108 >      this->rotationPropagation( integrableObjects[i], ji );
109  
110 <      dAtom->setJ( ji );
110 >      integrableObjects[i]->setJ( ji );
111      }
112    }
113  
# Line 114 | Line 118 | template<typename T> void NVT<T>::moveA() {
118    // Finally, evolve chi a half step (just like a velocity) using
119    // temperature at time t, not time t+dt/2
120  
121 +  //std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
122 +  
123    chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
124    integralOfChidt += chi*dt2;
125  
# Line 121 | Line 127 | template<typename T> void NVT<T>::moveB( void ){
127  
128   template<typename T> void NVT<T>::moveB( void ){
129    int i, j, k;
124 –  DirectionalAtom* dAtom;
130    double Tb[3], ji[3];
131    double vel[3], frc[3];
132    double mass;
# Line 132 | Line 137 | template<typename T> void NVT<T>::moveB( void ){
137  
138    oldChi = chi;
139  
140 <  for( i=0; i<nAtoms; i++ ){
140 >  for( i=0; i < integrableObjects.size(); i++ ){
141  
142 <    atoms[i]->getVel( vel );
142 >    integrableObjects[i]->getVel( vel );
143  
144      for (j=0; j < 3; j++)
145        oldVel[3*i + j]  = vel[j];
146  
147 <    if( atoms[i]->isDirectional() ){
147 >    if( integrableObjects[i]->isDirectional() ){
148  
149 <      dAtom = (DirectionalAtom *)atoms[i];
149 >      integrableObjects[i]->getJ( ji );
150  
146 –      dAtom->getJ( ji );
147 –
151        for (j=0; j < 3; j++)
152          oldJi[3*i + j] = ji[j];
153  
# Line 163 | Line 166 | template<typename T> void NVT<T>::moveB( void ){
166      chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
167        (tauThermostat*tauThermostat);
168  
169 <    for( i=0; i<nAtoms; i++ ){
169 >    for( i=0; i < integrableObjects.size(); i++ ){
170  
171 <      atoms[i]->getFrc( frc );
172 <      atoms[i]->getVel(vel);
171 >      integrableObjects[i]->getFrc( frc );
172 >      integrableObjects[i]->getVel(vel);
173  
174 <      mass = atoms[i]->getMass();
174 >      mass = integrableObjects[i]->getMass();
175  
176        // velocity half step
177        for (j=0; j < 3; j++)
178          vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
179  
180 <      atoms[i]->setVel( vel );
180 >      integrableObjects[i]->setVel( vel );
181  
182 <      if( atoms[i]->isDirectional() ){
182 >      if( integrableObjects[i]->isDirectional() ){
183  
181 –        dAtom = (DirectionalAtom *)atoms[i];
182 –
184          // get and convert the torque to body frame
185  
186 <        dAtom->getTrq( Tb );
187 <        dAtom->lab2Body( Tb );
186 >        integrableObjects[i]->getTrq( Tb );
187 >        integrableObjects[i]->lab2Body( Tb );
188  
189          for (j=0; j < 3; j++)
190            ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
191  
192 <        dAtom->setJ( ji );
192 >        integrableObjects[i]->setJ( ji );
193        }
194      }
195  
# Line 258 | Line 259 | template<typename T> double NVT<T>::getConservedQuanti
259    double thermostat_kinetic;
260    double thermostat_potential;
261  
262 <  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
262 >  fkBT = (double)(info->ndf) * kB * targetTemp;
263  
264    Energy = tStats->getTotalE();
265  
# Line 269 | Line 270 | template<typename T> double NVT<T>::getConservedQuanti
270  
271    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
272  
272 –  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
273 –      "\t" << thermostat_potential << "\t" << conservedQuantity << endl;
274 –
273    return conservedQuantity;
274   }
275  
# Line 280 | Line 278 | template<typename T> string NVT<T>::getAdditionalParam
278    const int BUFFERSIZE = 2000; // size of the read buffer
279    char buffer[BUFFERSIZE];
280  
281 <  sprintf(buffer,"\t%g\t%g;", chi, integralOfChidt);
281 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
282    parameters += buffer;
283  
284    return parameters;

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